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comparison phylogenomics_analysis.xml @ 15:34aa10ba20ef draft

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author greg
date Fri, 06 Jan 2017 14:14:12 -0500
parents a8a4f6009451
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14:a8a4f6009451 15:34aa10ba20ef
307 - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments. 307 - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments.
308 - **Sequence type used in the phylogenetic inference** - Sequence type used in the phylogenetic inference. 308 - **Sequence type used in the phylogenetic inference** - Sequence type used in the phylogenetic inference.
309 - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that 'Yes' was selected for the 'Create corresponding coding sequences?' option on the GeneFamilyClassifier tool when generating the selected input. This tool will produce an error if 'No' was selected. 309 - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that 'Yes' was selected for the 'Create corresponding coding sequences?' option on the GeneFamilyClassifier tool when generating the selected input. This tool will produce an error if 'No' was selected.
310 310
311 * **Phylogenetic trees options** 311 * **Phylogenetic trees options**
312
312 - **Phylogenetic trees inference method** - Phylogenetic trees inference method. 313 - **Phylogenetic trees inference method** - Phylogenetic trees inference method.
313 - **Select history item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees?** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup. 314 - **Select history item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees?** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup.
314 - **History item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees** -History item containing a set of string fragments matching sequences identifiers of species in the classification (including scaffold taxa) to be used for determining the most basal taxa in the orthogroups for rooting trees. The set of string fragments must be listed in decreasing order from older to younger lineages. 315 - **History item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees** -History item containing a set of string fragments matching sequences identifiers of species in the classification (including scaffold taxa) to be used for determining the most basal taxa in the orthogroups for rooting trees. The set of string fragments must be listed in decreasing order from older to younger lineages.
315 - **Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree** - Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree. 316 - **Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree** - Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree.
316 - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments. 317 - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments.
317 - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments 318 - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments
318 319
319 * **MSA quality control options** 320 * **MSA quality control options**
320 321
321 - **Remove gappy sequences in alignments?** - Removes gappy sites in alignments (e.g. 0.1 removes sites with 90% gaps). 322 - **Remove sequences with gaps of** - Removes gappy sequences in alignments (i.e., 0.5 removes sequences with 50% gaps).
323 - **Select process used for gap trimming** - Either nucleotide based trimming or alignments are trimed using using trimAl's ML heuristic trimming approach.
324 - **Remove sites in alignments with gaps of** - If the process used for gap trimming is nucleotide based, this is the gap value used when removing gappy sites in alignments (i.e., 0.1 removes sites with 90% gaps).
322 325
323 </help> 326 </help>
324 <citations> 327 <citations>
325 <citation type="bibtex"> 328 <citation type="bibtex">
326 @unpublished{None, 329 @unpublished{None,